Exploring the Heterogeneity of Non-Syndromic Hearing Loss: A Comprehensive Review of Implicated Genes and the Role of Whole Exome Sequencing

Authors

  • Mohammed M. Barrak College of Medicine, Wasit University, Iraq
  • Morteza Bonyadi Animal biology Department, faculty of natural sciences, University of Tabriz, Iran
  • Hasan Jasim Hami
  • Mohammed D. Al Ali
  • Riam Yousfe Muttair
  • Rawa Abdulkareem Abd

DOI:

https://doi.org/10.32792/utq/utjsci/v10i2.1143

Abstract

Background: Hereditary hearing loss (HHL) accounts for approximately 50-60% of all hearing loss (HL) cases, highlighting the significant role genetics play in this condition. HHL can be mostly classified into two main forms: syndromic and non-syndromic. Of these, non-syndromic hearing loss (NSHL) is the most prevalent, contributing to over 70% of HHL cases. The hearing process involves a complex interplay of various components inside the ear, working together to convert sound waves into comprehensible signals for the brain. Non-syndromic hearing loss (NSHL) is known for its extraordinary diversity and complexity, influenced by a vast array of genes, with more than 120 identified thus far. These genes can be categorized into distinct functional groups, encompassing cochlear ion homeostasis, hair bundle development and cell adhesion, synaptic transmission, transcriptional regulation, and mitochondrial function. The advent of next-generation sequencing (NGS) technologies has been instrumental in unraveling the genetic underpinnings of NSHL. Among NGS techniques, whole exome sequencing (WES) appeared as a revolutionary advancement, outperforming other approaches like targeted panel sequencing and whole-genome sequencing in terms of cost-effectiveness and efficiency. WES not only aids in deciphering the genetic basis of hearing loss but also offers the potential to revolutionize patient care and diagnosis. It paves the way for a new era for precision medicine in the realm of hearing loss, promising more accurate and tailored treatments for affected individuals. This transformative approach is poised to bring about substantial advancements in our understanding of hereditary hearing loss and its clinical management.

References

C. C. Morton and W. E. Nance, “Newborn hearing screening—a silent revolution,” N. Engl. J. Med., vol. 354, no. 20, pp. 2151–2164, 2006.

A. Kochhar, M. S. Hildebrand, and R. J. H. Smith, “Clinical aspects of hereditary hearing loss,” Genet. Med., vol. 9, no. 7, pp. 393–408, 2007.

I. Schrijver, “Hereditary non-syndromic sensorineural hearing loss: transforming silence to sound,” J. Mol. diagnostics, vol. 6, no. 4, pp. 275–284, 2004.

M. D. Venkatesh, N. Moorchung, and B. Puri, “Genetics of non syndromic hearing loss,” Med. J. armed forces india, vol. 71, no. 4, pp. 363–368, 2015.

S. Delmaghani and A. El-Amraoui, “Inner ear gene therapies take off: current promises and future challenges,” J. Clin. Med., vol. 9, no. 7, p. 2309, 2020.

Z. Jin, I. Uhlen, K. Wei-Jia, and D. Mao-Li, “Cochlear homeostasis and its role in genetic deafness,” J. Otol., vol. 4, no. 1, pp. 15–22, 2009.

X. Wu, W. Zhang, Y. Li, and X. Lin, “Structure and function of cochlear gap junctions and implications for the translation of cochlear gene therapies,” Front. Cell. Neurosci., vol. 13, p. 529, 2019.

D. J. Jagger and A. Forge, “Connexins and gap junctions in the inner ear–it’s not just about K+ recycling,” Cell Tissue Res., vol. 360, pp. 633–644, 2015.

T. Kikuchi, J. C. Adams, Y. Miyabe, E. So, and T. Kobayashi, “Potassium ion recycling pathway via gap junction systems in the mammalian cochlea and its interruption in hereditary nonsyndromic deafness,” Med. electron Microsc., vol. 33, pp. 51–56, 2000.

W. H. Evans and P. E. M. Martin, “Gap junctions: structure and function,” Mol. Membr. Biol., vol. 19, no. 2, pp. 121–136, 2002.

D. DeMille et al., “Three novel GJB2 (connexin 26) variants associated with autosomal dominant syndromic and nonsyndromic hearing loss,” Am. J. Med. Genet. Part A, vol. 176, no. 4, pp. 945–950, 2018.

F. Mammano, “Inner ear connexin channels: roles in development and maintenance of cochlear function,” Cold Spring Harb. Perspect. Med., vol. 9, no. 7, p. a033233, 2019.

P. Buonfiglio et al., “GJB 2 and GJB 6 genetic variant curation in an Argentinean non-syndromic hearing-impaired cohort,” Genes (Basel)., vol. 11, no. 10, p. 1233, 2020.

M. Cohen-Salmon et al., “Connexin30 deficiency causes instrastrial fluid–blood barrier disruption within the cochlear stria vascularis,” Proc. Natl. Acad. Sci., vol. 104, no. 15, pp. 6229–6234, 2007.

X.-Z. Liu et al., “Digenic inheritance of non-syndromic deafness caused by mutations at the gap junction proteins Cx26 and Cx31,” Hum. Genet., vol. 125, pp. 53–62, 2009.

M. Tekin, K. S. Arnos, and A. Pandya, “Advances in hereditary deafness,” Lancet, vol. 358, no. 9287, pp. 1082–1090, 2001.

H. Wang et al., “Targeted high-throughput sequencing identifies pathogenic mutations in KCNQ4 in two large Chinese families with autosomal dominant hearing loss,” PLoS One, vol. 9, no. 8, p. e103133, 2014.

S. L. Alper and A. K. Sharma, “The SLC26 gene family of anion transporters and channels,” Mol. Aspects Med., vol. 34, no. 2–3, pp. 494–515, 2013.

W. Reardon and R. Trembath, “Pendred syndrome.,” J. Med. Genet., vol. 33, no. 12, p. 1037, 1996.

L. X. Zhong, S. Kun, Q. Jing, C. Jing, and Y. Denise, “Non-syndromic hearing loss and high-throughput strategies to decipher its genetic heterogeneity,” J. Otol., vol. 8, no. 1, pp. 6–24, 2013.

B. Pan et al., “TMC1 forms the pore of mechanosensory transduction channels in vertebrate inner ear hair cells,” Neuron, vol. 99, no. 4, pp. 736–753, 2018.

D. P. Corey, N. Akyuz, and J. R. Holt, “Function and dysfunction of TMC channels in inner ear hair cells,” Cold Spring Harb. Perspect. Med., vol. 9, no. 10, 2019.

S. Rayat, M. Farhadi, H. Emamdjomeh, S. Morovvati, and M. Falah, “Analysis of TMIE gene mutations including the first large deletion of exon 1 with autosomal recessive non-syndromic deafness,” BMC Med. Genomics, vol. 15, no. 1, pp. 1–10, 2022.

T. G. Markova et al., “Clinical features of hearing loss caused by STRC gene deletions/mutations in Russian population,” Int. J. Pediatr. Otorhinolaryngol., vol. 138, p. 110247, 2020.

S. Han, D. Zhang, Y. Guo, Z. Fu, and G. Guan, “Prevalence and characteristics of STRC gene mutations (DFNB16): A systematic review and meta-analysis,” Front. Genet., vol. 12, p. 707845, 2021.

H. Bolz et al., “Mutation of CDH23, encoding a new member of the cadherin gene family, causes Usher syndrome type 1D,” Nat. Genet., vol. 27, no. 1, pp. 108–112, 2001.

J. M. Bork et al., “Usher syndrome 1D and nonsyndromic autosomal recessive deafness DFNB12 are caused by allelic mutations of the novel cadherin-like gene CDH23,” Am. J. Hum. Genet., vol. 68, no. 1, pp. 26–37, 2001.

V. Mermall, P. L. Post, and M. S. Mooseker, “Unconventional myosins in cell movement, membrane traffic, and signal transduction,” Science (80-. )., vol. 279, no. 5350, pp. 527–533, 1998.

R. Nambiar, R. E. McConnell, and M. J. Tyska, “Myosin motor function: the ins and outs of actin-based membrane protrusions,” Cell. Mol. life Sci., vol. 67, pp. 1239–1254, 2010.

P. K. Legan and G. P. Richardson, “Extracellular matrix and cell adhesion molecules in the developing inner ear,” in Seminars in Cell & Developmental Biology, 1997, vol. 8, no. 3, pp. 217–224.

P. K. Legan et al., “Three deaf mice: mouse models for TECTA-based human hereditary deafness reveal domain-specific structural phenotypes in the tectorial membrane,” Hum. Mol. Genet., vol. 23, no. 10, pp. 2551–2568, 2014.

P. K. Legan, V. A. Lukashkina, R. J. Goodyear, M. Kössl, I. J. Russell, and G. P. Richardson, “A targeted deletion in α-tectorin reveals that the tectorial membrane is required for the gain and timing of cochlear feedback,” Neuron, vol. 28, no. 1, pp. 273–285, 2000.

T. Ikezono, A. Omori, S. Ichinose, R. Pawankar, A. Watanabe, and T. Yagi, “Identification of the protein product of the Coch gene (hereditary deafness gene) as the major component of bovine inner ear protein,” Biochim. Biophys. Acta (BBA)-Molecular Basis Dis., vol. 1535, no. 3, pp. 258–265, 2001.

E. Gallant et al., “Novel COCH mutation in a family with autosomal dominant late onset sensorineural hearing impairment and tinnitus,” Am. J. Otolaryngol., vol. 34, no. 3, pp. 230–235, 2013.

K. T. Booth et al., “Novel loss-of-function mutations in COCH cause autosomal recessive nonsyndromic hearing loss,” Hum. Genet., vol. 139, pp. 1565–1574, 2020.

S. Oleskevich and B. Walmsley, “Synaptic transmission in the auditory brainstem of normal and congenitally deaf mice,” J. Physiol., vol. 540, no. 2, pp. 447–455, 2002.

B. Vona, A. Rad, and E. Reisinger, “The many faces of DFNB9: relating OTOF variants to hearing impairment,” Genes (Basel)., vol. 11, no. 12, p. 1411, 2020.

L. De Vries, X. Lou, G. Zhao, B. Zheng, and M. G. Farquhar, “GIPC, a PDZ domain containing protein, interacts specifically with the C terminus of RGS-GAIP,” Proc. Natl. Acad. Sci., vol. 95, no. 21, pp. 12340–12345, 1998.

M. Katoh, “Functional proteomics, human genetics and cancer biology of GIPC family members,” Exp. Mol. Med., vol. 45, no. 6, pp. e26–e26, 2013.

H. Azaiez et al., “Genomic landscape and mutational signatures of deafness-associated genes,” Am. J. Hum. Genet., vol. 103, no. 4, pp. 484–497, 2018.

C. M. Sloan-Heggen et al., “Comprehensive genetic testing in the clinical evaluation of 1119 patients with hearing loss,” Hum. Genet., vol. 135, pp. 441–450, 2016.

S. A. Lambert et al., “The human transcription factors,” Cell, vol. 172, no. 4, pp. 650–665, 2018.

S. Wayne et al., “Mutations in the transcriptional activator EYA4 cause late-onset deafness at the DFNA10 locus,” Hum. Mol. Genet., vol. 10, no. 3, pp. 195–200, 2001.

L. Wang et al., “Eya4 regulation of Na+/K+-ATPase is required for sensory system development in zebrafish,” 2008.

T. Makishima et al., “Nonsyndromic hearing loss DFNA10 and a novel mutation of EYA4: evidence for correlation of normal cardiac phenotype with truncating mutations of the Eya domain,” Am. J. Med. Genet. Part A, vol. 143, no. 14, pp. 1592–1598, 2007.

M. Pfister et al., “A 4bp-insertion in the eya-homologous region (eyaHR) of EYA4 causes hearing impairment in a Hungarian family linked to DFNA10,” Mol. Med., vol. 8, no. 10, pp. 607–611, 2002.

J. Schönberger et al., “Dilated cardiomyopathy and sensorineural hearing loss: a heritable syndrome that maps to 6q23–24,” Circulation, vol. 101, no. 15, pp. 1812–1818, 2000.

S.-J. Choi et al., “Clinical and molecular characterizations of novel POU3F4 mutations reveal that DFN3 is due to null function of POU3F4 protein,” 2009.

V. Malik, D. Zimmer, and R. Jauch, “Diversity among POU transcription factors in chromatin recognition and cell fate reprogramming,” Cell. Mol. Life Sci., vol. 75, pp. 1587–1612, 2018.

E. Bernardinelli et al., “Novel POU3F4 variants identified in patients with inner ear malformations exhibit aberrant cellular distribution and lack of SLC6A20 transcriptional upregulation,” Front. Mol. Neurosci., vol. 15, p. 999833, 2022.

Y. Su et al., “Clinical and molecular characterization of POU3F4 mutations in multiple DFNX2 Chinese families,” BMC Med. Genet., vol. 19, no. 1, pp. 1–10, 2018.

L. Sennaroğlu and M. D. Bajin, “Incomplete partition type III: a rare and difficult cochlear implant surgical indication,” Auris Nasus Larynx, vol. 45, no. 1, pp. 26–32, 2018.

H. Kokotas, M. B. Petersen, and P. J. Willems, “Mitochondrial deafness,” Clin. Genet., vol. 71, no. 5, pp. 379–391, 2007.

X. Estivill et al., “Familial progressive sensorineural deafness is mainly due to the mtDNA A1555G mutation and is enhanced by treatment with aminoglycosides,” Am. J. Hum. Genet., vol. 62, no. 1, pp. 27–35, 1998.

J. Foster II and M. Tekin, “Aminoglycoside induced ototoxicity associated with mitochondrial DNA mutations,” Egypt. J. Med. Hum. Genet., vol. 17, no. 3, pp. 287–293, 2016.

Y. Bykhovskaya et al., “Evidence for complex nuclear inheritance in a pedigree with nonsyndromic deafness due to a homoplasmic mitochondrial mutation,” Am. J. Med. Genet., vol. 77, no. 5, pp. 421–426, 1998.

K. B. Sevior et al., “Mitochondrial A7445G mutation in two pedigrees with palmoplantar keratoderma and deafness,” Am. J. Med. Genet., vol. 75, no. 2, pp. 179–185, 1998.

M. Nakamura et al., “A novel point mutation in the mitochondrial tRNASer (UCN) gene detected in a family with MERRF/MELAS overlap syndrome,” Biochem. Biophys. Res. Commun., vol. 214, no. 1, pp. 86–93, 1995.

M. M. Li et al., “Clinical evaluation and etiologic diagnosis of hearing loss: A clinical practice resource of the American College of Medical Genetics and Genomics (ACMG),” Genet. Med., vol. 24, no. 7, pp. 1392–1406, 2022.

N. H. Robin, “It does matter: the importance of making the diagnosis of a genetic syndrome,” Curr. Opin. Pediatr., vol. 18, no. 6, pp. 595–597, 2006.

M. D. Ali, M. M. Barrak, R. I. Salman, and N. M. Sa’doon, “The combined effect of artemisia absinthium methanolic extract and vinblastine chemotherapy on apoptosis and decreasing chemotherapy drug concentration,” in AIP Conference Proceedings, 2023, vol. 2845, no. 1.

J. W. Brunger, G. S. Murray, M. O’Riordan, A. L. Matthews, R. J. H. Smith, and N. H. Robin, “Parental attitudes toward genetic testing for pediatric deafness,” Am. J. Hum. Genet., vol. 67, no. 6, pp. 1621–1625, 2000.

N. H. Robin, S. K. Prucka, A. L. Woolley, and R. J. H. Smith, “The use of genetic testing in the evaluation of hearing impairment in a child,” Curr. Opin. Pediatr., vol. 17, no. 6, pp. 709–712, 2005.

J. M. Rizzo and M. J. Buck, “Key principles and clinical applications of ‘next-generation’ DNA sequencing,” Cancer Prev. Res., vol. 5, no. 7, pp. 887–900, 2012.

D. Yan, M. Tekin, S. H. Blanton, and X. Z. Liu, “Next-generation sequencing in genetic hearing loss,” Genet. Test. Mol. Biomarkers, vol. 17, no. 8, pp. 581–587, 2013.

B. Rabbani, M. Tekin, and N. Mahdieh, “The promise of whole-exome sequencing in medical genetics,” J. Hum. Genet., vol. 59, no. 1, pp. 5–15, 2014.

A. Martini, F. Sorrentino, U. Sorrentino, and M. Cassina, “Genetics & Epigenetics of Hereditary Deafness: An Historical Overview,” Audiol. Res., vol. 11, no. 4, pp. 629–635, 2021.

T. Atik, G. Bademci, O. Diaz-Horta, S. H. Blanton, and M. Tekin, “Whole-exome sequencing and its impact in hereditary hearing loss,” Genet. Res. (Camb)., vol. 97, p. e4, 2015.

T. B. Friedman and A. J. Griffith, “Human nonsyndromic sensorineural deafness,” Annu. Rev. Genomics Hum. Genet., vol. 4, no. 1, pp. 341–402, 2003.

A. E. Shearer and R. J. H. Smith, “Genetics: advances in genetic testing for deafness,” Curr. Opin. Pediatr., vol. 24, no. 6, p. 679, 2012.

O. Diaz-Horta et al., “Whole-exome sequencing efficiently detects rare mutations in autosomal recessive nonsyndromic hearing loss,” PLoS One, vol. 7, no. 11, p. e50628, 2012.

Downloads

Published

2023-12-27

Issue

Section

Review

Categories

How to Cite

Exploring the Heterogeneity of Non-Syndromic Hearing Loss: A Comprehensive Review of Implicated Genes and the Role of Whole Exome Sequencing. (2023). University of Thi-Qar Journal of Science, 10(2), 192-199. https://doi.org/10.32792/utq/utjsci/v10i2.1143